CRISPR Pipeline - README

Overview

The pipeline includes downloading raw sequencing data, processing it, and identifying genetic variants.

Prerequisites

Ensure that the following tools are installed on your system:

• wget: Used to download raw sequencing data and reference genomes.
• gunzip: For decompressing .gz files.
• FastQC: For quality control of raw reads.
• fastp: For trimming sequencing reads.
• BWA: For aligning the sequencing reads to a reference genome.
• samtools: For sorting, removing duplicates, and converting file formats.
• GATK: For variant calling.
• picard-tools: Required for file format conversion and preparing BAM files for GATK.
• SnpEff: For variant annotation.
• VEP: Used for annotating variants based on the genome.

(Step 3) During Quality Control check the following parameters:

1. Per base sequence quality
2. Overrepresented sequences
3. Adapter content

(Step 4) For Trimming These are the Universal Adapters: Illumina Universal Adapter = AGATCGGAAGAG
Illumina Small RNA 3' Adapter = TGGAATTCTCGG
Illumina Small RNA 5' Adapter = GATCGTCGGACT
Nextera Transposase Sequence = CTGTCTCTTATA
PolyA = AAAAAAAAAAAA
PolyG = GGGGGGGGGGGG

Open newly created adapter.fasta file in Notepad and write:

>H1
AGATCGGAAGAG